| Previous changeset 0:88c1516e25e0 (2019-04-03) Next changeset 2:01750c193a83 (2019-10-25) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142" |
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modified:
scanpy-run-umap.xml |
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added:
scanpy_macros2.xml |
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| diff -r 88c1516e25e0 -r 0ac2f9f2313b scanpy-run-umap.xml --- a/scanpy-run-umap.xml Wed Apr 03 11:10:27 2019 -0400 +++ b/scanpy-run-umap.xml Mon Sep 16 08:16:59 2019 -0400 |
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| @@ -2,50 +2,46 @@ <tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy1"> <description>visualise cell clusters using UMAP</description> <macros> - <import>scanpy_macros.xml</import> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-run-umap.py - -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' - #if $embeddings - --output-embeddings-file embeddings.csv +PYTHONIOENCODING=utf-8 scanpy-run-umap + --use-graph '${use_graph}' + --key-added '${key_added}' +#if $embeddings + --export-embedding embeddings.csv +#end if +#if $settings.default == "false" + --n-components ${settings.n_components} + --min-dist ${settings.min_dist} + --spread ${settings.spread} + --alpha ${settings.alpha} + --gamma ${settings.gamma} + --negative-sample-rate ${settings.negative_sample_rate} + --random-state ${settings.random_seed} + #if $settings.init_pos + --init-pos '${settings.init_pos}' #end if - #if $settings.default == "false" - -n '${settings.n_components}' - --min-dist '${settings.min_dist}' - --spread '${settings.spread}' - --alpha '${settings.alpha}' - --gamma '${settings.gamma}' - --negative-sample-rate '${settings.negative_sample_rate}' - #if $settings.init_pos - --init-pos '${settings.init_pos}' - #end if - #if $settings.maxiter - --maxiter '${settings.maxiter}' - #end if - #if $settings.a - -a '${settings.a}' - #end if - #if $settings.b - -b '${settings.b}' - #end if - #if $settings.random_seed is not None - -s '${settings.random_seed}' - #end if - #end if + #if $settings.maxiter + --maxiter ${settings.maxiter} + #end if +#end if + @INPUT_OPTS@ + @OUTPUT_OPTS@ -@PLOT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/> + <param name="use_graph" argument="--use-graph" value="neighbors" type="text" + label="Name of the slot that holds the KNN graph"/> + <param name="key_added" argument="--key-added" type="text" optional="true" + label="Additional suffix to the name of the slot to save the embedding"/> + <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> @@ -62,26 +58,13 @@ <option value="random">random</option> </param> <param name="maxiter" argument="--maxiter" type="integer" optional="true" label="Number of iterations of optimisation"/> - <param name="a" argument="-a" type="float" optional="true" label="More specific parameter controlling embedding, automatically determined from --min-dist and --spread if unset"/> - <param name="b" argument="-b" type="float" optional="true" label="More specific parameter controlling embedding, automatically determined from --min-dist and --spread if unset"/> - <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for numpy random number generator"/> + <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/> </when> </conditional> - <conditional name="do_plotting"> - <param name="plot" type="boolean" checked="false" label="Make UMAP plot"/> - <when value="true"> - <expand macro="output_plot_params"/> - <param name="color_by" argument="--color-by" type="text" value="louvain" label="Color by attributes, comma separated strings"/> - </when> - <when value="false"/> - </conditional> </inputs> <outputs> <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: UMAP object"/> - <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: UMAP plot"> - <filter>do_plotting['plot']</filter> - </data> <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: UMAP embeddings"> <filter>embeddings</filter> </data> @@ -95,10 +78,7 @@ <param name="default" value="false"/> <param name="embeddings" value="true"/> <param name="random_seed" value="0"/> - <param name="plot" value="true"/> - <param name="color_by" value="louvain"/> <output name="output_h5" file="run_umap.h5" ftype="h5" compare="sim_size"/> - <output name="output_png" file="run_umap.png" ftype="png" compare="sim_size"/> <output name="output_embed" file="run_umap.embeddings.csv" ftype="csv" compare="sim_size"> <assert_contents> <has_n_columns n="2" sep=","/> @@ -108,9 +88,12 @@ </tests> <help><![CDATA[ -======================================================== -Embed the neighborhood graph using UMAP (`tl.umap`) -======================================================== +========================================================== +Embed the neighborhood graph using UMAP (`scanpy.tl.umap`) +========================================================== + +For making UMAP plots, please use `Scanpy PlotEmbed` with the output of this tool and enter "umap" as the +name of the embedding to plot. UMAP (Uniform Manifold Approximation and Projection) is a manifold learning technique suitable for visualizing high-dimensional data. Besides tending to |
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| diff -r 88c1516e25e0 -r 0ac2f9f2313b scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 16 08:16:59 2019 -0400 |
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| @@ -0,0 +1,94 @@ +<macros> + <token name="@TOOL_VERSION@">1.4.2</token> + <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2). + +1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. + +1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. + ]]></token> + <token name="@INPUT_OPTS@"> + --input-format '${input_format}' input.h5 + </token> + <token name="@OUTPUT_OPTS@"> + --show-obj stdout --output-format '${output_format}' output.h5 + </token> + <token name="@PLOT_OPTS@"> +#if $fig_title + --title '${fig_title}' +#end if + --fig-size '${fig_size}' + --fig-dpi ${fig_dpi} + --fig-fontsize ${fig_fontsize} + ${fig_frame} + ./output.png + </token> + <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.2.4.post4">scanpy-scripts</requirement> + <yield/> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <yield /> + <citation type="doi">10.1186/s13059-017-1382-0</citation> + <citation type="bibtex"> + @misc{githubscanpy-scripts, + author = {Ni Huang, EBI Gene Expression Team}, + year = {2018}, + title = {Scanpy-scripts: command line interface for Scanpy}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/scanpy-scripts}, + }</citation> + </citations> + </xml> + + <xml name="input_object_params"> + <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 format"/> + <param name="input_format" argument="--input-format" type="select" label="Format of input object"> + <option value="anndata" selected="true">AnnData format hdf5</option> + <option value="loom">Loom format hdf5</option> + </param> + </xml> + + <xml name="output_object_params"> + <param name="output_format" argument="--output-format" type="select" label="Format of output object"> + <option value="anndata" selected="true">AnnData format hdf5</option> + <option value="loom">Loom format hdf5</option> + </param> + </xml> + + <xml name="output_plot_params"> + <param name="fig_title" argument="--title" type="text" label="Figure title"/> + <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/> + <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/> + <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/> + <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false" + label="Show plot frame"/> + </xml> + + <xml name="export_mtx_params"> + <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/> + </xml> + + <xml name="export_mtx_outputs"> + <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix"> + <filter>export_mtx</filter> + </data> + <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes"> + <filter>export_mtx</filter> + </data> + <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes"> + <filter>export_mtx</filter> + </data> + </xml> +</macros> |